No, it does not have to do with installed too many apps as the apps are installed on the data-partition and not to the system-partition. My Data-partition has 11 MByte free (without making any modifications since flashing the new firmware)
I just checked again /system/app: only superuser.apk is installed by me, nothing else.
But I make free another 6 MByte by deleting EbookDemo.apk and EbookDemo.odex
Edit: Perhaps someone without Link2sd can check and post the free space on /system after the firmware upgrade to see whats left afterwards.